Software

NetProphet 2.0

NetProphet 2.0, building on NetProphet 1.0, is a "data light" algorithm for mapping transcription factor networks from gene expression data and annotated genome sequence. It has been shown to have high accuracy on both yeast and fruit fly.

NetSurgeon

NetSurgeon is a novel algorithm for transcriptome engineering -- designing transcription-factor deletions or over-expressions to move cells to a gene expression state that is associated with a desired phenotype.

NetProphet

NetProphet is a novel algorithm for inferring transcriptional regulatory networks from gene expression data. For every possible interaction between a TF and a target gene, NetProphet computes a confidence score by combining the score from its coexpression analysis with the score from its DE analysis.

PhenoProphet

PhenoProphet is a novel algorithm that assigns each TF in a network a score representing the confidence that the deletion of that TF will yield a phenotypic change of interest. Given a network, the PhenoProphet score of a TF for a phenotype or interest is based on the enrichment of the TF's targets for genes that are known to be linked to the phenotype of interest.

GRENDEL

GRENDEL (Gene Regulatory Network Decoding Evaluations tooL), generates random gene regulatory networks according to user defined constraints on the network topology and kinetics. It then simulates the state of each regulatory network under various user defined conditions (the experimental design) and produces simulated gene expression data.

Second release for the GRENDEL benchmark tool. Improvements include: support for gcc4, improved build process and error handling, and the addition of model compilation scripts to easily render a table of gene expression data from a model path.

primerD

The primerD program implements a novel algorithm for the design of unique degenerate primer pairs. Using primers designed by primerD it is possible to reduce the total number of primers that need to be amplified by over 35% while amplifying the same number of targets. This program has a highly configurable set of parameters that account for both basic PCR and degenerate primer constraints. As a final verification of primer pair efficacy an extensive mis-priming check is done to ensure the uniqueness of each intended amplification.

eval

Eval is a flexible tool for analyzing the performance of gene-structure prediction programs. It provides summaries and graphical distributions for many statistics describing any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another.

PPFINDER

PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence. In gene prediction mode, PPFINDER will mask out the genomic sequence and rerun gene prediction. Rounds of pseudogene masking and gene prediction are iterated until convergence.

Validate GTF

GTF (gene transfer format) is a simple, precise format for annotating protein coding genes which has been used for a number of multi-group annotation efforts. It is a specialized subset of GFF (general feature format). The specification for GTF can be found here.

If a GTF file contains errors, programs that parse it can yield false conclusions. Validate GTF is a flexible Perl script that checks a GTF file for correctness. It can detect most common syntactic errors, such as including the stop codon within the CDS annotation. It can also detect semantic errors, such as annotated coding sequence that contains stop codons spanning splice sites.

Twinscan/N-SCAN

Twinscan/N-SCAN is our lab's suite of software for gene-structure prediction. We recommend running N-SCAN on our web server (http://mblab.wustl.edu/nscan). Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci. N-SCAN is available for human and Drosophila (fruitfly).